Comparison of proteome between porcine pancreatic ductal organoids of different passages and donor ages. Organoids were derived from Embryonic, early postnatal and adult animals and cultured. For the early postnatal derived organoids, early and late passages were used to isolate proteins and investigate proteomic differences.
## on all contrastsres_ora2 <-test_ORA(se_data, by_contrast = T, species ="Human", type ="KEGG", pAdjustMethod ="BH", pvalueCutoff =0.1 )
774 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
10 gene(s) do not match in database.
848 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
11 gene(s) do not match in database.
767 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
9 gene(s) do not match in database.
Star enrich KEGG terms on 3 clusters: PN_earlyP_vs_PN_lateP;PN_lateP_vs_Adult;PN_lateP_vs_Embryo with 777;851;770 ENTREZIDs.
Code
enrichplot::dotplot(res_ora2, showCategory =20) +ggtitle(paste("Over Representation Analysis of", sample_name),subtitle ="Human KEGG Pathways") +theme(plot.title =element_text(hjust =0.5, size =16, face ="bold", family ="Arial", margin =margin(t =15, b =10)),axis.text.y =element_text(size =5, margin =margin(t =10, l =10, b =1)))+scale_fill_gradient(low ="#55b2cf", high ="#d63cba")+theme_cowplot()
Code
if (save) {ggsave(filename =paste(date, figname, "ORA_all_contrasts_kegg.pdf", sep ="_", collapse =""), device ="pdf",height =26, width =16, path = fig_dir)# Extract all ORA results as a data frameas.data.frame(res_ora2) %>%write_xlsx(path =paste(path_results ,paste( figname, "ORA_all_contrasts_kegg.xlsx", sep ="_"), sep ="/"))}
6.2 GO
Code
## Dotplot function from DOSE packageres_ora2 <-test_ORA(se_data, by_contrast = T, species ="Human", type ="GO", pAdjustMethod ="BH",pvalueCutoff =0.1 )
774 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
10 gene(s) do not match in database.
848 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
11 gene(s) do not match in database.
767 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
9 gene(s) do not match in database.
Star enrich GO terms on 3 clusters: PN_earlyP_vs_PN_lateP;PN_lateP_vs_Adult;PN_lateP_vs_Embryo with 777;851;770 ENTREZIDs.
Code
enrichplot::dotplot(res_ora2, showCategory =20) +ggtitle(paste("Over Representation Analysis of", sample_name),subtitle ="Human KEGG Pathways") +theme(plot.title =element_text(hjust =0.5, size =16, face ="bold", family ="Arial", margin =margin(t =15, b =10)),axis.text.y =element_text(size =5, margin =margin(t =10, l =10, b =1)))+scale_fill_gradient(low ="#55b2cf", high ="#d63cba")+theme_cowplot()
Code
if (save) {ggsave(filename =paste(date, figname, "ORA_all_contrasts_GO.pdf", sep ="_", collapse =""), device ="pdf",height =26, width =16, path = fig_dir)# Extract all ORA results as a data frameas.data.frame(res_ora2) %>%write_xlsx(path =paste(path_results ,paste( figname, "ORA_all_contrasts_GO.xlsx", sep ="_"), sep ="/"))}
6.3 Reactome
Code
## Dotplot function from DOSE packageres_ora2 <-test_ORA(se_data, by_contrast = T, species ="Human", type =c("REACTOME"), pAdjustMethod ="BH",pvalueCutoff =0.1 )
774 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
10 gene(s) do not match in database.
848 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
11 gene(s) do not match in database.
767 gene(s) transfrom to ENTREZID from SYMBOL. 3 gene(s) transfrom to ENTREZID from ALIAS.
9 gene(s) do not match in database.
Star enrich REACTOME terms on 3 clusters: PN_earlyP_vs_PN_lateP;PN_lateP_vs_Adult;PN_lateP_vs_Embryo with 777;851;770 ENTREZIDs.
Code
enrichplot::dotplot(res_ora2, showCategory =20) +ggtitle(paste("Over Representation Analysis of", str_replace_all(sample_name, "_", " ")),subtitle ="Pig Reactome Pathways") +theme(plot.title =element_text(hjust =0.5, size =12, face ="bold", family ="Arial"),axis.text.y =element_text(size =2, ))+scale_fill_gradientn(colours =viridis(10, begin =0.25, end =0.9))+scale_fill_gradient(low ="#196f8a", high ="#d63cba")+theme_cowplot()
8297 gene(s) transfrom to ENTREZID from SYMBOL. 6 gene(s) transfrom to ENTREZID from ALIAS.
74 gene(s) do not match in database.
wdw
Code
## Dotplot function from DOSE packageenrichplot::dotplot(res_gsea, showCategory =10)+scale_fill_gradientn(colours =viridis(10, begin =0.25, end =0.9))+ggtitle(paste("GSEA of", str_replace_all(sample_name, "_", " ")),subtitle ="Human GO Pathways")+scale_fill_gradient(low ="#196f8a", high ="#d63cba")+theme_cowplot()
8297 gene(s) transfrom to ENTREZID from SYMBOL. 6 gene(s) transfrom to ENTREZID from ALIAS.
74 gene(s) do not match in database.
hsaaaa
Code
## Dotplot function from DOSE packageenrichplot::dotplot(res_gsea, showCategory =10)+scale_fill_gradientn(colours =viridis(10, begin =0.25, end =0.9))+ggtitle(paste("GSEA of", str_replace_all(sample_name, "_", " ")),subtitle ="Human KEGG Pathways")+scale_fill_gradient(low ="#196f8a", high ="#d63cba")+theme_cowplot()
8297 gene(s) transfrom to ENTREZID from SYMBOL. 6 gene(s) transfrom to ENTREZID from ALIAS.
74 gene(s) do not match in database.
Code
## Dotplot function from DOSE packageenrichplot::dotplot(res_gsea, showCategory =10)+scale_fill_gradientn(colours =viridis(10, begin =0.2, end =0.9))+ggtitle(paste("GSEA of", str_replace_all(sample_name, "_", " ")),subtitle ="Human Reactome Pathways")+scale_fill_gradient(low ="#196f8a", high ="#d63cba")+theme_cowplot()